I installed a 5.5" RE long arm 3 link lift in my jeep and I am in the process of getting shocks and installing them. My lift came with new shock mount brackets for the axle. I will be using these. ( Im not running the stock axle). I havent looked real close yet but it looks like the new RE mounts will mount higher on the axle. My ? is. Do I want to run a shock that is made for 5-6" lift or do I want to run a 4" lift shock because the mounts make the distance shorter?

I guess what I am worried about is bottoming out the shock when it is fully compressed and not hitting the bump stop yet. If anyone knows a good shock to run or has some part numbers that would be great. Thanks.

I would think you would want the shorter shocks as your distance is shorter.
I would give Dirk over at DPGoffroad a call on what exact shock would work best for ya.
He deals in R/E and OME so he should be the guy for the job.